In south-east Asia, during Quaternary glaciations, increased seasonality and sea level decreases of ~120 m caused considerable fragmentation of the rainforest. It is believed that most of the region's core was covered with savannah vegetation, and rainforest was confined to a few refugia. We investigated the geographical extent of the savannah vegetation and the positions of the refugia, using a combination of palynonlogical, geological, fossil and termite data. Our results show that during the Last Glacial Maximum, most of Thailand, Peninsula Malaysia, western and southern Borneo, eastern and southern Sumatra, and Java were probably covered by savannah. Rainforest refugia were probably present in northern and eastern Borneo, northern and western Sumatra and the Mentawai islands. We also discuss a possible complete history of the region. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 75, 453–466.